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RAD seq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al . (2016)
Author(s) -
McKinney Garrett J.,
Larson Wesley A.,
Seeb Lisa W.,
Seeb James E.
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12649
Subject(s) - biology , linkage disequilibrium , genome , evolutionary biology , adaptation (eye) , disequilibrium , selection (genetic algorithm) , computational biology , restriction enzyme , molecular ecology , restriction site , genetics , linkage (software) , ecology , dna , gene , haplotype , machine learning , population , allele , computer science , medicine , neuroscience , ophthalmology , demography , sociology
In their recently corrected manuscript, “Breaking RAD : An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation”, Lowry et al . argue that genome scans using RAD seq will miss many loci under selection due to a combination of sparse marker density and low levels of linkage disequilibrium in most species. We agree that marker density and levels of LD are important considerations when designing a RAD seq study; however, we dispute that RAD ‐based genome scans are as prone to failure as Lowry et al . suggest. Their arguments ignore the flexible nature of RAD seq; the availability of different restriction enzymes and capacity for combining restriction enzymes ensures that a well‐designed study should be able to generate enough markers for efficient genome coverage. We further believe that simplifying assumptions about linkage disequilibrium in their simulations are invalid in many species. Finally, it is important to note that the alternative methods proposed by Lowry et al . have limitations equal to or greater than RAD seq. The wealth of studies with positive impactful findings that have used RAD genome scans instead supports the argument that properly conducted RAD genome scans are an effective method for gaining insight into ecology and evolution, particularly for non‐model organisms and those with large or complex genomes.